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Background  The acquisition of iron is important for the pathogenicity of bacteria and blood. Three different culture environments (Fe stimulation, blood agar plate and normal plate) were used to stimulate  Enterobacter cloacae , and their respective pathogenicities were compared at the proteomic, mRNA and metabolomic levels.    Methods  2D-DIGE combined with MALDI-TOF-MS/MS, RT-PCR and  1 H NMR were used to analyze the differential expression levels of proteins, mRNA and metabolites.    Results  A total of 109 proteins were identified by 2D-DIGE and mass spectrometry after pairwise comparison within three culture environments, clustered into 3 classes and 183 functional categories, which were involved in 23 pathways. Based on the 2D-DIGE results, multiple proteins were selected for verification by mRNA expression. These results confirmed that most of the proteins were regulated at the transcriptional level. Thirty-eight metabolites were detected by NMR, which correlated with the differentially expressed proteins under different treatment conditions.    Conclusions  The results show that culture in a blood agar plate and a suitable concentration of iron promote the pathogenicity of  E. cloacae  and that high iron concentrations may have adverse effects on growth and iron uptake and utilization by  E. cloacae .    Electronic supplementary material  The online version of this article (doi:10.1186/s12953-016-0104-y) contains supplementary material, which is available to authorized users.

Multi-omics analysis on the pathogenicity of Enterobacter cloacae ENHKU01 isolated from sewage outfalls along the Ningbo coastline